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NMR assignments of the macro domain from severe acute respiratory syndrome coronavirus 2 (SARS-CoV-2) Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-24 Meng-Hsuan Lin, Yi-Ping Huang, Chi-Fon Chang, Chun-Hua Hsu
SARS-CoV-2 is a novel pathogen causing pneumonia named COVID-19 and leading to a severe pandemic since the end of 2019. The genome of SARS-CoV-2 contains a macro domain that may play an important role in regulating ADP-ribosylation in host cells and initiating viral replication. Here, we report the 1H, 13C, and 15N resonance assignments of the SARS-CoV-2 macro domain. This work provides the ground
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Backbone and ILVM methyl resonance assignments of human thymidylate synthase in apo and substrate bound forms Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-24 Jeffrey P. Bonin, Andrew L. Lee
Human thymidylate synthase (hTS) is a 72 kDa homodimeric enzyme responsible for the conversion of deoxyuridine monophosphate (dUMP) to deoxythymidine monophosphate (dTMP), making it the sole source of de novo dTMP in human cells. As a result, hTS is an attractive anti-cancer therapeutic target. Additionally, hTS is known to possess a number of interesting biophysical features, including adoption of
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1 H, 13 C and 15 N chemical shift assignment of the stem-loop 5a from the 5′-UTR of SARS-CoV-2 Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-23 Robbin Schnieders, Stephen A. Peter, Elnaz Banijamali, Magdalena Riad, Nadide Altincekic, Jasleen Kaur Bains, Betül Ceylan, Boris Fürtig, J. Tassilo Grün, Martin Hengesbach, Katharina F. Hohmann, Daniel Hymon, Bozana Knezic, Andreas Oxenfarth, Katja Petzold, Nusrat S. Qureshi, Christian Richter, Judith Schlagnitweit, Andreas Schlundt, Harald Schwalbe, Elke Stirnal, Alexey Sudakov, Jennifer Vögele,
The SARS-CoV-2 (SCoV-2) virus is the causative agent of the ongoing COVID-19 pandemic. It contains a positive sense single-stranded RNA genome and belongs to the genus of Betacoronaviruses. The 5′- and 3′-genomic ends of the 30 kb SCoV-2 genome are potential antiviral drug targets. Major parts of these sequences are highly conserved among Betacoronaviruses and contain cis-acting RNA elements that affect
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1 H, 13 C and 15 N backbone chemical shift assignments of SARS-CoV-2 nsp3a Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-21 Nicola Salvi, Luiza Mamigonian Bessa, Serafima Guseva, Aldo Camacho-Zarco, Damien Maurin, Laura Marino Perez, Anas Malki, Martin Hengesbach, Sophie Marianne Korn, Andreas Schlundt, Harald Schwalbe, Martin Blackledge
The non-structural protein nsp3 from SARS-CoV-2 plays an essential role in the viral replication transcription complex. Nsp3a constitutes the N-terminal domain of nsp3, comprising a ubiquitin-like folded domain and a disordered acidic chain. This region of nsp3a has been linked to interactions with the viral nucleoprotein and the structure of double membrane vesicles. Here, we report the backbone resonance
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1 H, 13 C, and 15 N NMR chemical shift assignment of the complex formed by the first EPEC EspF repeat and N-WASP GTPase binding domain Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-21 Mikael Karjalainen, Maarit Hellman, Helena Tossavainen, Perttu Permi
LEE-encoded effector EspF (EspF) is an effector protein part of enteropathogenic Escherichia coli’s (EPEC’s) arsenal for intestinal infection. This intrinsically disordered protein contains three highly conserved repeats which together compose over half of the protein’s complete amino acid sequence. EPEC uses EspF to hijack host proteins in order to promote infection. In the attack EspF is translocated
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NMR assignments of the N -glycans of the Fc fragment of mouse immunoglobulin G2b glycoprotein Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-10 Saeko Yanaka, Yoshiki Yamaguchi, Takeshi Takizawa, Yohei Miyanoiri, Rina Yogo, Ichio Shimada, Koichi Kato
The Fc portion of immunoglobulin G (IgG) promotes defensive effector functions in the immune system by interacting with Fcγ receptors and complement component C1q. These interactions critically depend on N-glycosylation at Asn297 of each CH2 domain, where biantennary complex-type oligosaccharides contain microheterogeneities resulting primarily from the presence or absence of non-reducing terminal
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Backbone assignment of E. coli NfsB and the effects of addition of the cofactor analogue nicotinic acid Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-09 Eva I. Hyde, Alex Ka-Wing Chau, Lorna J. Smith
E. coli nitroreductase NfsB (also called NfnB) has been studied extensively, largely due to its potential for cancer gene therapy. A homodimeric flavoprotein of 216 residues, it catalyses the reduction of nitroaromatics to cytotoxic hydroxylamines by NADH and NADPH and also the reduction of quinones to hydroxyquinones. Its role in vivo is not known but it is postulated to be involved in reducing oxidative
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1 H, 13 C and 15 N chemical shift assignments of the SUD domains of SARS-CoV-2 non-structural protein 3c: “The SUD-M and SUD-C domains” Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-09 Angelo Gallo, Aikaterini C. Tsika, Nikolaos K. Fourkiotis, Francesca Cantini, Lucia Banci, Sridhar Sreeramulu, Harald Schwalbe, Georgios A. Spyroulias
SARS-CoV-2 RNA, nsP3c (non-structural Protein3c) spans the sequence of the so-called SARS Unique Domains (SUDs), first observed in SARS-CoV. Although the function of this viral protein is not fully elucidated, it is believed that it is crucial for the formation of the replication/transcription viral complex (RTC) and of the interaction of various viral “components” with the host cell; thus, it is essential
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1H, 15N, and 13C backbone resonance assignments of the C4b-binding region from the S. aureus extracellular adherence protein Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-09 Indrani Pal, Nitin Mishra, Alvaro I. Herrera, Abhinav Dubey, Haribabu Arthanari, Brian V. Geisbrecht, Om Prakash
The Extracellular Adherence Protein (Eap) from Staphylococcus aureus is a potent inhibitor of the classical and lectin pathways of the complement system. Previous studies have shown that Eap binds with nanomolar affinity to complement component C4b and prevents C4b binding the pro-protease, C2, thereby inhibiting formation of the pro-C3 convertase shared by the classical and lectin pathways (Woehl
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NMR assignments for the C-terminal domain of human TDP-43 Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-08 David Pantoja-Uceda, Cristiana Stuani, Douglas V. Laurents, Ann E. McDermott, Emanuele Buratti, Miguel Mompeán
Transactive response DNA-binding protein of 43 kDa (TDP-43) is a 414-residue protein whose aberrant aggregation is implicated in neurodegenerative diseases, including amyotrophic lateral sclerosis (ALS) or frontotemporal lobar degeneration (FTLD). Intriguingly, TDP-43 has also been shown to functionally oligomerize to carry out physiological functions. TDP-43 also exists in mixed condensates or granules
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Resonance assignments and secondary structure of thermophile single‐stranded DNA binding protein from Sulfolobus solfataricus at 323K Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-06 Min June Yang, Woonghee Lee, Chin-Ju Park
Single-stranded DNA (ssDNA)-binding proteins (SSBs) are essential for DNA replication, recombination, and repair processes in all organisms. Sulfolobus solfataricus (S. solfataricus), a hyperthermophilic species, overexpresses its SSB (S. solfataricus SSB (SsoSSB)) to protect ssDNA during DNA metabolisms. Even though the crystal structure of apo SsoSSB and its ssDNA-bound solution structure have been
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Correction to: Backbone and side chain NMR assignments of the H-NOX domain from Nostoc sp. in complex with BAY58-2667 (cinaciguat) Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-05 Garyfallia I. Makrynitsa, Aikaterini I. Argyriou, Georgios Dalkas, Dimitra A. Georgopoulou, Marina Bantzi, Athanassios Giannis, Andreas Papapetropoulos, Georgios A. Spyroulias
In the original publication of the article, the Acknowledgements section was omitted. The section is as follows:
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Resonance assignments of the cytoplasmic domain of ECF sigma factor W pathway protein YsdB from Bacillus subtilis Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-04 Yanqing Li, GuangLin Li, Zhihao Wang, Wei Chen, Hongliang Wang, Yawen Wang, Bing Liu
Bacterial sigma (σ) factor, along with RNA polymerase core enzyme, initiates gene transcription from specific promoter regions and therefore regulates clusters of genes in response to a particular situation. The extracytoplasmic function (ECF) σ factors are a class of alternative σ factors that are often associated with environmental signal transduction across the bacterial membrane, in which external
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NMR assignments of vaccinia virus protein A28: an entry-fusion complex component Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-04 Danni Wu, Yuan-Chao Lou, Wen Chang, Der-Lii M. Tzou
Vaccinia virus (VACV) belonging to the poxvirus family enters the host cell via two different entry pathways; either endocytosis or virus/host cell membrane fusion. With respect to the virus/host cell membrane fusion, there are eleven viral membrane proteins forming a complicated entry-fusion complex (EFC), including A28, A21, A16, F9, G9, G3, H2, J5, L5, L1 and O3, to conduct the fusion function.
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Backbone chemical shift assignments for the SARS-CoV-2 non-structural protein Nsp9: intermediate (ms – μs) dynamics in the C-terminal helix at the dimer interface Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-04 Garry W. Buchko, Mowei Zhou, Justin K. Craig, Wesley C. Van Voorhis, Peter J. Myler
The Betacoronavirus SARS-CoV-2 non-structural protein Nsp9 is a 113-residue protein that is essential for viral replication, and consequently, a potential target for the development of therapeutics against COVID19 infections. To capture insights into the dynamics of the protein’s backbone in solution and accelerate the identification and mapping of ligand-binding surfaces through chemical shift perturbation
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1 H, 15 N and 13 C resonance assignments of the N-terminal domain of the nucleocapsid protein from the endemic human coronavirus HKU1 Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-03 Aline de Luna Marques, Icaro Putinhon Caruso, Marcos Caique Santana-Silva, Peter Reis Bezerra, Gabriela Rocha Araujo, Fabio Ceneviva Lacerda Almeida, Gisele Cardoso Amorim
Coronaviruses have become of great medical and scientific interest because of the Covid-19 pandemic. The hCoV-HKU1 is an endemic betacoronavirus that causes mild respiratory symptoms, although the infection can progress to severe lung disease and death. During viral replication, a discontinuous transcription of the genome takes place, producing the subgenomic messenger RNAs. The nucleocapsid protein
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1 H, 13 C, and 15 N resonance assignments of reduced apo-WhiB4 from Mycobacterium tuberculosis Biomol. NMR Assign. (IF 0.677) Pub Date : 2021-01-03 Qiran Zhai, Chen Lin, Bo Duan, Jun Liu, Lu Zhang, Bin Xia
The WhiB4 protein, a member of WhiB-like proteins, plays an important role in the survival and pathology of Mycobacterium tuberculosis (Mtb). As a transcription factor, WhiB4 regulates the expression of genes involved in maintaining redox homeostasis, central metabolism, and respiration. Furthermore, WhiB4 leads to the condensation of mycobacterial nucleoids and is capable of binding to DNA. WhiB4
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Assignment of the Ile, Leu, Val, Met and Ala methyl group resonances of the DEAD-box RNA helicase DbpA from E. coli Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-12-04 Jan Philip Wurm
ATP-dependent DEAD-box helicases constitute one of the largest families of RNA helicases and are important regulators of most RNA-dependent cellular processes. The functional core of these enzymes consists of two RecA-like domains. Changes in the interdomain orientation of these domains upon ATP and RNA binding result in the unwinding of double-stranded RNA. The DEAD-box helicase DbpA from E. coli
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1 H, 13 C, and 15 N backbone chemical shift assignments of the C-terminal dimerization domain of SARS-CoV-2 nucleocapsid protein Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-12-03 Sophie M. Korn, Roderick Lambertz, Boris Fürtig, Martin Hengesbach, Frank Löhr, Christian Richter, Harald Schwalbe, Julia E. Weigand, Jens Wöhnert, Andreas Schlundt
The current outbreak of the highly infectious COVID-19 respiratory disease is caused by the novel coronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus 2). To fight the pandemic, the search for promising viral drug targets has become a cross-border common goal of the international biomedical research community. Within the international Covid19-NMR consortium, scientists support drug
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Backbone and nearly complete side-chain chemical shift assignments of the human death-associated protein 1 (DAP1) Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-12-02 Christoph Wiedemann, Johanna Voigt, Jan Jirschitzka, Sabine Häfner, Oliver Ohlenschläger, Frank Bordusa
Death-associated protein 1 (DAP1) is a proline-rich cytoplasmatic protein highly conserved in most eukaryotes. It has been reported to be involved in controlling cell growth and migration, autophagy and apoptosis. The presence of human DAP1 is associated to a favourable prognosis in different types of cancer. Here we describe the almost complete \({{^{1}}\text {H}}\), \({{^{13}}\text {C}}\), and \({{^{15}}\text
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1 H, 13 C and 15 N chemical shift assignments of the SUD domains of SARS-CoV-2 non-structural protein 3c: “the N-terminal domain-SUD-N” Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-11-23 Angelo Gallo, Aikaterini C. Tsika, Nikolaos K. Fourkiotis, Francesca Cantini, Lucia Banci, Sridhar Sreeramulu, Harald Schwalbe, Georgios A. Spyroulias
Among the proteins encoded by the SARS-CoV-2 RNA, nsP3 (non-structural Protein3) is the largest multi-domain protein. Its role is multifaceted and important for the viral life cycle. Nonetheless, regarding the specific role of each domain there are many aspects of their function that have to be investigated. SARS Unique Domains (SUDs), constitute the nsP3c region of the nsP3, and were observed for
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1 H, 13 C, and 15 N backbone and side chain chemical shift assignments of the SARS-CoV-2 non-structural protein 7 Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-11-20 Marco Tonelli, Chad Rienstra, Thomas K. Anderson, Rob Kirchdoerfer, Katherine Henzler-Wildman
The SARS-CoV-2 genome encodes for approximately 30 proteins. Within the international project covid19-nmr, we distribute the spectroscopic analysis of the viral proteins and RNA. Here, we report NMR chemical shift assignments for the protein nsp7. The 83 amino acid nsp7 protein is an essential cofactor in the RNA-dependent RNA polymerase. The polymerase activity and processivity of nsp12 are greatly
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1 H, 13 C, 15 N resonance assignment of the apo form of the small, chitin-active lytic polysaccharide monooxygenase Jd LPMO10A from Jonesia denitrificans Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-11-19 Idd A. Christensen, Vincent G. H. Eijsink, Finn L. Aachmann, Gaston Courtade
The lytic polysaccharide monooxygenase JdLPMO10A is the N-terminal domain of the multimodular protein Jd1381. The isolated JdLPMO10A domain is one of the smallest chitin-active lytic polysaccharide monooxygenases known to date with a size of only 15.5 kDa. JdLPMO10A is a copper-dependent oxidative enzyme that depolymerizes chitin by hydroxylating the C1 carbon in the glycosidic bond. JdLPMO10A has
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NMR resonance assignments of the FinO-domain of the RNA chaperone RocC Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-11-11 Reiner Eidelpes, Hyeong Jin Kim, J. N. Mark Glover, Martin Tollinger
In prokaryotic species, gene expression is commonly regulated by small, non-coding RNAs (sRNAs). In the gram-negative bacterium Legionella pneumophila, the regulatory, trans-acting sRNA molecule RocR base pairs with a complementary sequence in the 5’-untranslated region of mRNAs encoding for proteins in the bacterial DNA uptake system, thereby controlling natural competence. Sense-antisense duplexing
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1 H, 13 C, and 15 N backbone chemical shift assignments of coronavirus-2 non-structural protein Nsp10 Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-11-07 N. Kubatova, N. S. Qureshi, N. Altincekic, R. Abele, J. K. Bains, B. Ceylan, J. Ferner, C. Fuks, B. Hargittay, M. T. Hutchison, V. de Jesus, F. Kutz, M. A. Wirtz Martin, N. Meiser, V. Linhard, D. J. Pyper, S. Trucks, B. Fürtig, M. Hengesbach, F. Löhr, C. Richter, K. Saxena, A. Schlundt, H. Schwalbe, S. Sreeramulu, A. Wacker, J. E. Weigand, J. Wirmer-Bartoschek, J. Wöhnert
The international Covid19-NMR consortium aims at the comprehensive spectroscopic characterization of SARS-CoV-2 RNA elements and proteins and will provide NMR chemical shift assignments of the molecular components of this virus. The SARS-CoV-2 genome encodes approximately 30 different proteins. Four of these proteins are involved in forming the viral envelope or in the packaging of the RNA genome and
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Backbone and side chain NMR assignments of the H-NOX domain from Nostoc sp. in complex with BAY58-2667 (cinaciguat) Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-10-30 Garyfallia I. Makrynitsa, Aikaterini I. Argyriou, Georgios Dalkas, Dimitra A. Georgopoulou, Marina Bantzi, Athanassios Giannis, Andreas Papapetropoulos, Georgios A. Spyroulias
Soluble guanylate cyclase (sGC) enzyme is activated by the gaseous signaling agent nitric oxide (NO) and triggers the conversion of GTP (guanosine 5′-triphosphate) to cGMP (cyclic guanylyl monophosphate). It contains the heme binding H-NOX (heme-nitric oxide/oxygen binding) domain which serves as the sensor of NO and it is highly conserved across eukaryotes and bacteria as well. Many research studies
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13 C and 15 N chemical shift assignments of A117V and M129V human Y145Stop prion protein amyloid fibrils Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-10-29 Hanh H. Dao, May Z. Hlaing, Yixuan Ma, Krystyna Surewicz, Witold K. Surewicz, Christopher P. Jaroniec
The C-terminally truncated Y145Stop variant of prion protein (PrP23-144) has been linked to a heritable prionopathy in humans and is also capable of triggering a transmissible prion disease in mice. PrP23-144 can be converted from soluble monomeric form to amyloid under physiological conditions, providing an in vitro model for investigating the molecular basis of amyloid strains and cross-seeding barriers
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Resonance assignments of La protein RRM domain from Trypanosoma brucei Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-10-21 Fangzhen Shan, Nannan Zhang
The autoantigen La protein is a conserved component of eukaryotic ribonucleoprotein complexes that binds the 3′ poly(U) sequences of nascent RNA polymerase III transcripts to assist folding and maturation. This specific recognition is mediated by the N-terminal domain (NTD) of La, which comprises a La motif and an RNA recognition motif (RRM). Here, we report near complete 1H, 13C and 15N backbone and
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1 H N , 13 C, and 15 N resonance assignments of the Clostridioides difficile receptor binding domain 2 (CDTb, residues 757–876) Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-10-09 Mary E. Cook, Kristen M. Varney, Raquel Godoy-Ruiz, David J. Weber
Clostridioides difficile is a bacterial pathogen responsible for the majority of nosocomial infections in the developed world. C. difficile infection (CDI) is difficult to treat in many cases because hypervirulent strains have evolved that contain a third toxin, termed the C. difficile toxin (CDT), in addition to the two enterotoxins TcdA and TcdB. CDT is a binary toxin comprised of an enzymatic,
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Solid state NMR assignments of a human λ-III immunoglobulin light chain amyloid fibril. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-09-18 Tejaswini Pradhan,Karthikeyan Annamalai,Riddhiman Sarkar,Ute Hegenbart,Stefan Schönland,Marcus Fändrich,Bernd Reif
The aggregation of antibody light chains is linked to systemic light chain (AL) amyloidosis, a disease where amyloid deposits frequently affect the heart and the kidney. We here investigate fibrils from the λ-III FOR005 light chain (LC), which is derived from an AL-patient with severe cardiac involvement. In FOR005, five residues are mutated with respect to its closest germline gene segment IGLV3-19
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NMR resonance assignment and backbone dynamics of a C-terminal domain homolog of orange carotenoid protein. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-09-16 Eugene G Maksimov,Gennady Yu Laptev,Dmitriy S Blokhin,Vladimir V Klochkov,Yury B Slonimskiy,Nikolai N Sluchanko,Thomas Friedrich,Chi-Fon Chang,Vladimir I Polshakov
Photoprotection in cyanobacteria is mediated by the Orange Carotenoid Protein (OCP), a two-domain photoswitch which has multiple natural homologs of its N- and C-terminal domains. Recently, it was demonstrated that C-terminal domain homologs (CTDHs) of OCP are standalone carotenoproteins participating in multidirectional carotenoid transfer between membranes and proteins. Non-covalent embedment of
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Backbone and side-chain chemical shift assignments of p50 subunit of NF-κB transcription factor. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-09-16 Amrinder Singh,H Jane Dyson
Nuclear Factor κB (NF-κB) is a family of five related transcription factors that recognize a κB DNA element on the promoter and enhancer regions of target genes and modulate their expression. Here we report a complete set of 1H, 13C, 15N backbone and side chain resonance assignments for the p50 DNA binding and dimerization domains of the p50 homodimer form of the NF-κB transcription factor. The chemical
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1H, 13C, 15 N backbone resonance assignment of the recognition lobe subdomain 3 (Rec3) from Streptococcus pyogenes CRISPR-Cas9. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-09-15 Erin Skeens,Kyle W East,George P Lisi
Rec3 is a subdomain of the recognition (Rec) lobe within CRISPR (Clustered Regularly Interspaced Short Palindromic Repeats)-associated protein Cas9 that is involved in nucleic acid binding and is critical to HNH endonuclease activation. Here, we report the backbone resonance assignments of an engineered construct of the Rec3 subdomain from Streptococcus pyogenes Cas9. We also analyze backbone chemical
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1H, 13C and 15N resonance assignment of the YTH domain of YTHDC2. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-09-15 Fahu He,Ryuta Endo,Kanako Kuwasako,Mari Takahashi,Kengo Tsuda,Takashi Nagata,Satoru Watanabe,Akiko Tanaka,Naohiro Kobayashi,Takanori Kigawa,Peter Güntert,Mikako Shirouzu,Shigeyuki Yokoyama,Yutaka Muto
In humans, YTH (YT521-B homology) domain containing protein 2 (YTHDC2) plays a crucial role in the phase-shift from mitosis to meiosis. YTH domains bind to methylated adenosine nucleotides such as m6A. In a phylogenic tree, the YTH domain of YTHDC2 (YTH2) and that of the YTH containing protein YTHDC1 (YTH1) belong to the same sub-group. However, the binding affinity of m6A differs between these proteins
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[Formula: see text]H, [Formula: see text]C and [Formula: see text]N assignments of human Grb2 free of ligands. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-08-25 Louise Pinet,Ying-Hui Wang,Anaïs Vogel,Françoise Guerlesquin,Nadine Assrir,Carine van Heijenoort
Growth factor receptor-bound 2 (Grb2) is an important link in the receptor tyrosine kinase signaling cascades. It is involved in crucial processes, both physiological (mainly embryogenesis) and pathological (different types of cancer). Several binding partners of all three domains (SH3–SH2–SH3) of this adaptor protein are well described, such as ErbB family members for the SH2 domain and Sos for the
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1H, 13C, and 15N backbone chemical shift assignments of the apo and the ADP-ribose bound forms of the macrodomain of SARS-CoV-2 non-structural protein 3b. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-08-14 F Cantini,L Banci,N Altincekic,J K Bains,K Dhamotharan,C Fuks,B Fürtig,S L Gande,B Hargittay,M Hengesbach,M T Hutchison,S M Korn,N Kubatova,F Kutz,V Linhard,F Löhr,N Meiser,D J Pyper,N S Qureshi,C Richter,K Saxena,A Schlundt,H Schwalbe,S Sreeramulu,J-N Tants,A Wacker,J E Weigand,J Wöhnert,A C Tsika,N K Fourkiotis,G A Spyroulias
The SARS-CoV-2 genome encodes for approximately 30 proteins. Within the international project COVID19-NMR, we distribute the spectroscopic analysis of the viral proteins and RNA. Here, we report NMR chemical shift assignments for the protein Nsp3b, a domain of Nsp3. The 217-kDa large Nsp3 protein contains multiple structurally independent, yet functionally related domains including the viral papain-like
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1H, 13C, and 15N backbone chemical shift assignments of the nucleic acid-binding domain of SARS-CoV-2 non-structural protein 3e. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-08-08 Sophie M Korn,Karthikeyan Dhamotharan,Boris Fürtig,Martin Hengesbach,Frank Löhr,Nusrat S Qureshi,Christian Richter,Krishna Saxena,Harald Schwalbe,Jan-Niklas Tants,Julia E Weigand,Jens Wöhnert,Andreas Schlundt
The ongoing pandemic caused by the Betacoronavirus SARS-CoV-2 (Severe Acute Respiratory Syndrome Coronavirus-2) demonstrates the urgent need of coordinated and rapid research towards inhibitors of the COVID-19 lung disease. The covid19-nmr consortium seeks to support drug development by providing publicly accessible NMR data on the viral RNA elements and proteins. The SARS-CoV-2 genome encodes for
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Nearly complete 1H, 13C and 15N chemical shift assignment of monomeric form of N-terminal domain of Nephila clavipes major ampullate spidroin 2. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-08-06 Nur Alia Oktaviani,Ali D Malay,Akimasa Matsugami,Fumiaki Hayashi,Keiji Numata
Spider dragline silk is well recognized due to its excellent mechanical properties. Dragline silk protein mainly consists of two proteins, namely, major ampullate spidroin 1 (MaSp1) and major ampullate spidroin 2 (MaSp2). The MaSp N-terminal domain (NTD) conformation displays a strong dependence on ion and pH gradients, which is crucial for the self-assembly behavior of spider silk. In the spider major
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1H, 13C and 15N resonance assignments for the microtubule-binding domain of the kinetoplastid kinetochore protein KKT4 from Trypanosoma brucei. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-07-21 Patryk Ludzia,Bungo Akiyoshi,Christina Redfield
KKT4 is a kinetoplastid-specific microtubule-binding kinetochore protein that lacks significant similarity to any known kinetochore or microtubule-binding proteins. Here we present the 1H, 13C and 15N resonance assignments for several fragments from the microtubule-binding domain of KKT4 (KKT4115–343) from Trypanosoma brucei. These assignments provide the starting point for detailed investigations
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Backbone and sidechain NMR assignments for the ribosome maturation factor RbfA from Escherichia coli. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-07-15 Andreas Schedlbauer,Idoia Iturrioz,Borja Ochoa-Lizarralde,Retina Çapuni,Xu Han,Elisa de Astigarraga,Tammo Diercks,Paola Fucini,Sean R Connell
RbfA (ribosome binding factor A; 15.2 kDa) is a protein involved in ribosome biogenesis and has been shown to be important for growth at low temperatures and to act as a suppressor for a cold-sensitive mutation (C23U) in the ribosomal RNA of the small 30S ribosomal subunit. The 3D structure of isolated RbfA has been determined from several organisms showing that RbfA has type-II KH-domain fold topology
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Correction to: 1H, 13C, 15N backbone and IVL methyl group resonance assignment of the fungal β-glucosidase from Trichoderma reesei. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-07-11 Eleni Makraki,Marta G Carneiro,Alex Heyam,Eiso Ab,Gregg Siegal,Roderick E Hubbard
In the original publication of the article, the name of one of the authors is incorrect. The author's name is Eiso AB, but was modified to A. B. Eiso. The correct name is given in this Correction.
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Correction to: Resonance assignments of a VapC family toxin from Clostridium thermocellum. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-07-09 Chen Wang,Jinsong Xuan,Qiu Cui,Yingang Feng
In the original publication of the article, the authors found a misquote in the Reference section.
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Backbone and sidechain resonance assignments and secondary structure of Scc4 from Chlamydia trachomatis. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-07-02 Thilini O Ukwaththage,Marco Tonelli,Megan A Macnaughtan
Chlamydia trachomatis is an obligate intracellular bacterium that causes the most common sexually transmitted bacterial diseases in the world. With a biphasic developmental cycle, the bacteria utilize a type III secretion system (T3SS) to invade host cells as infectious elemental bodies, which then differentiate into actively dividing reticulate bodies. The regulation of the developmental cycle and
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Resonance assignment of the outer membrane protein AlkL in lipid bilayers by proton-detected solid-state NMR. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-30 Tobias Schubeis,Tom S Schwarzer,Tanguy Le Marchand,Jan Stanek,Kumar Tekwani Movellan,Kathrin Castiglione,Guido Pintacuda,Loren B Andreas
Most commonly small outer membrane proteins, possessing between 8 and 12 β-strands, are not involved in transport but fulfill diverse functions such as cell adhesion or binding of ligands. An intriguing exception are the 8-stranded β-barrel proteins of the OmpW family, which are implicated in the transport of small molecules. A representative example is AlkL from Pseudomonas putida GPoI, which functions
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1H, 13C and 15N backbone resonance assignment of BRCA1 fragment 219-504. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-24 Michał Górka,Szymon Żerko,Robert Konrat,Wiktor Koźmiński,Dennis Kurzbach
The breast cancer susceptibility protein 1 (BRCA1) plays a central role in the suppression of human breast and ovarian cancer. Germ line mutations of the BRCA1 gene are responsible for the hereditary breast and ovarian cancer (HBOC) syndrome. Here were report 1H, 13C, and 15N resonance assignments for the intrinsically disordered BRCA1 fragment 219–504, which contains important interaction sites for
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NMR resonance assignments of the programmed cell death protein 5 (PDCD5) from Toxoplasma gondii. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-23 Meng-Hsuan Lin,Tsun-Ai Yu,Chi-Fon Chang,Yoshifumi Nishikawa,Chun-Hua Hsu
Toxoplasmosis is a systematic protozoan disease caused by a tiny parasite Toxoplasma gondii. The infection can be dangerous for pregnant woman and people with weak immune systems. The secreted protein named TgPDCD5 (Programmed cell death protein 5 from Toxoplasma gondii) plays an important role in apoptosis-inducing effect on host cells. Here, we report the 1H, 13C, and 15N resonance assignments of
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Backbone resonance assignment and dynamics of 110 kDa hexameric inorganic pyrophosphatase from Mycobacterium tuberculosis. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-19 Roman S Romanov,Sofia S Mariasina,Sergey V Efimov,Vladimir V Klochkov,Elena V Rodina,Vladimir I Polshakov
Family I soluble inorganic pyrophosphatases (PPases; EC 3.6.1.1) are enzymes essential for all organisms. They hydrolyze inorganic pyrophosphate, thus providing the driving force for numerous biosynthetic reactions. Soluble PPases retain enzymatic activity only in multimeric forms. PPases from various organisms are extensively studied by X-ray crystallography but until now there was no information
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1H, 13C, 15N backbone and IVL methyl group resonance assignment of the fungal β-glucosidase from Trichoderma reesei. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-19 Eleni Makraki,Marta G Carneiro,Alex Heyam,A B Eiso,Gregg Siegal,Roderick E Hubbard
β-glucosidases have received considerable attention due to their essential role in bioethanol production from lignocellulosic biomass. β-glucosidase can hydrolyse cellobiose in cellulose degradation and its low activity has been considered as one of the main limiting steps in the process. Large-scale conversions of cellulose therefore require high enzyme concentration which increases the cost. β-glucosidases
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1H, 13C, and 15N backbone assignments of the C-terminal region of the human retinoic acid-induced protein 2. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-18 Andras Lang,Nishit Goradia,Harriet Wikman,Stefan Werner,Matthias Wilmanns,Oliver Ohlenschläger
Retinoic acid-induced protein 2 is a human protein of 530 residues encoded by the RAI2 gene (Q9Y5P3; RAI2_HUMAN). RAI2 is a novel tumor suppressor protein whose depletion in breast cancer cell lines results in the downregulation of several genes associated with differentiation along with increased invasiveness and aggressive tumor phenotype of the cells. The role of the protein is specified to be a
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Backbone resonance assignments of the catalytic and regulatory domains of Ca2+/calmodulin-dependent protein kinase 1D. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-13 Michael H G Tong,Mark Jeeves,Sundaresan Rajesh,Christian Ludwig,Marc Lenoir,Jitendra Kumar,Darren M McClelland,Fedor Berditchevski,Julia A Hubbard,Colin Kenyon,Sam Butterworth,Stefan Knapp,Michael Overduin
The CaMK subfamily of Ser/Thr kinases are regulated by calmodulin interactions with their C-terminal regions. They are exemplified by Ca2+/calmodulin dependent protein kinase 1δ which is known as CaMK1D, CaMKIδ or CKLiK. CaMK1D mediates intracellular signalling downstream of Ca2+ influx and thereby exhibits amplifications of Ca2+signals and polymorphisms that have been implicated in breast cancer and
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1H, 13C, and 15N backbone chemical shift assignments of m7GTP cap-bound Leishmania initiation factor 4E-1. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-09 Anissa Belfetmi,Mélissa Léger-Abraham
Most of the translational control of gene expression in higher eukaryotes occurs during the initiation step of protein synthesis. While this process is well characterized in mammalian cells, it is less defined in parasites, including the ones that cause human Leishmaniasis. The Leishmania cap-binding isoform 1 (LeishIF4E-1) is the only isoform that binds the specific trypanosomatids-specific hypermethylated
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Backbone and side-chain chemical shift assignments of a cellular FLICE-inhibitory protein (c-FLIPS). Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-06 Zhi-Qiang Bai,Bin Liu,Xiaofang Ma,Kaifeng Hu
Cellular FLICE-inhibitory protein (c-FLIP), which is involved in regulating the apoptosis of the extrinsic cell death pathway contains two death effector domains (DED). There are several splicing variants including short-form (c-FLIPS) and long-form (c-FLIPL). The death-inducing signaling complex (DISC) initiates apoptosis and programmed necrosis, DISC assembly and activation are regulated by c-FLIP
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1H, 13C and 15 N NMR assignments of solubility tag protein Msyb of Escherichia coli. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-05 Yanan Yang,Zunhui Ke,Zhihao Wang,Yanqing Li,Yan Li,Yawen Wang,Bing Liu
Biochemical and structural characterizations of a protein are the prerequisite for the further understanding of its biological role and potential applications. The expression of recombinant protein is almost unavoidable to produce the amount of the protein required for these studies, especially at the industrial level. Escherichia coli is the single most used system for recombinant protein expression
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1H, 15N and 13C resonance assignments of the HR1c domain of PRK1, a protein kinase C-related kinase. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-04 Georgios Sophocleous,George Wood,Darerca Owen,Helen R Mott
PRK1 is a member of the protein kinase C-related kinase (PRK) family of serine/threonine kinases and a downstream effector of Rho GTPases. PRK1 has three N-terminal Homology Region 1 (HR1) domains (HR1a, HR1b and HR1c), which form antiparallel coiled coils that interact with Rho family GTPases. PRK1 also has a C2-like domain that targets it to the plasma membrane and a kinase domain, which is a member
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1H, 13C and 15N resonance assignments of Q38FZ4, hypothetical protein from Trypanosoma brucei. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-03 Rui Wang,Jiahai Zhang,Shanhui Liao,Xiaoming Tu
Q38FZ4 (UniProt accession number), is an 85-residue hypothetical protein from Trypanosoma brucei (T. brucei). Q38FZ4, which might be specific among the trypanosomatid genomes, shares low sequence similarity with mammal proteins and also has an essential function in the growth of T. brucei. Here we report the resonance assignments and secondary structure analysis of Q38FZ4 from T. brucei, which will
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1H, 13C, 15N backbone resonance assignments of the apo and holo forms of the ABC transporter solute binding protein PiuA from Streptococcus pneumoniae. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-06-03 Katherine A Edmonds,Yifan Zhang,Daniel J Raines,Anne-K Duhme-Klair,David P Giedroc
Streptococcus pneumoniae is a Gram-positive human pathogen that causes millions of infections worldwide with an increasing occurrence of antibiotic resistance. Iron acquisition is essential for its survival and virulence, especially under host-imposed nutritional immunity. S. pneumoniae expresses several ATP-binding cassette (ABC) transporters to facilitate acquisition under iron limitation, including
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1H, 13C and 15N NMR chemical shift assignments of cAMP-regulated phosphoprotein-19 and -16 (ARPP-19 and ARPP-16). Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-05-28 Chandan J Thapa,Tatu Haataja,Ulla Pentikäinen,Perttu Permi
Protein Phosphatase 2A, PP2A, the principal Serine/threonine phosphatase, has major roles in broad range of signaling pathways that include regulation of cell cycle, cell proliferation and neuronal signaling. The loss of function of PP2A is linked with many human diseases, like cancer and neurodegenerative disorders. Protein phosphatase 2A (PP2A) functions as tumor suppressor and its tumor suppressor
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Resonance assignments and secondary structure prediction of secretory protein Rv0603 from Mycobacterium tuberculosis H37Rv. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-05-20 Sarita Tripathi,Rahul Yadav,Anupam Jain,Surya V S R K Pulavarti,Prem Prakash Pathak,Ajaya Kumar Behera,Ashish Arora
We report the NMR resonance assignments of N-terminal signal sequence deleted secretory protein Rv0603 (∆1–28−Rv0603) from Mycobacterium tuberculosis H37Rv. ∆1–28−Rv0603 displayed good peak yield and signal dispersion in 2D [15N-1H] HSQC spectrum, which prompted us to proceed for resonance assignments on this construct. Standard triple-resonance experiments for resonance assignments were recorded on
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1H, 13C and 15N assignment of the paramagnetic high potential iron-sulfur protein (HiPIP) PioC from Rhodopseudomonas palustris TIE-1. Biomol. NMR Assign. (IF 0.677) Pub Date : 2020-05-15 Inês B Trindade,Michele Invernici,Francesca Cantini,Ricardo O Louro,Mario Piccioli
High potential iron–sulfur proteins (HiPIPs) are a class of small proteins (50–100 aa residues), containing a 4Fe–4S iron–sulfur cluster. The 4Fe–4S cluster shuttles between the oxidation states [Fe4S4]3+/2+, with a positive redox potential in the range (500–50 mV) throughout the different known HiPIPs. Both oxidation states are paramagnetic at room temperature. HiPIPs are electron transfer proteins